head 1.2; access; symbols pkgsrc-2026Q1:1.2.0.24 pkgsrc-2026Q1-base:1.2 pkgsrc-2025Q4:1.2.0.22 pkgsrc-2025Q4-base:1.2 pkgsrc-2025Q3:1.2.0.20 pkgsrc-2025Q3-base:1.2 pkgsrc-2025Q2:1.2.0.18 pkgsrc-2025Q2-base:1.2 pkgsrc-2025Q1:1.2.0.16 pkgsrc-2025Q1-base:1.2 pkgsrc-2024Q4:1.2.0.14 pkgsrc-2024Q4-base:1.2 pkgsrc-2024Q3:1.2.0.12 pkgsrc-2024Q3-base:1.2 pkgsrc-2024Q2:1.2.0.10 pkgsrc-2024Q2-base:1.2 pkgsrc-2024Q1:1.2.0.8 pkgsrc-2024Q1-base:1.2 pkgsrc-2023Q4:1.2.0.6 pkgsrc-2023Q4-base:1.2 pkgsrc-2023Q3:1.2.0.4 pkgsrc-2023Q3-base:1.2 pkgsrc-2023Q2:1.2.0.2 pkgsrc-2023Q2-base:1.2 pkgsrc-2023Q1:1.1.0.10 pkgsrc-2023Q1-base:1.1 pkgsrc-2022Q4:1.1.0.8 pkgsrc-2022Q4-base:1.1 pkgsrc-2022Q3:1.1.0.6 pkgsrc-2022Q3-base:1.1 pkgsrc-2022Q2:1.1.0.4 pkgsrc-2022Q2-base:1.1 pkgsrc-2022Q1:1.1.0.2 pkgsrc-2022Q1-base:1.1; locks; strict; comment @# @; 1.2 date 2023.05.17.21.55.34; author bacon; state Exp; branches; next 1.1; commitid 27fZ134VGLb3FmpE; 1.1 date 2022.03.17.16.01.12; author bacon; state Exp; branches; next ; commitid Q8UklxdSfTDWnAwD; desc @@ 1.2 log @biology/hisat2: Add SIMDE support SIMDE enables SSE and other x86 intrinsics on other architectures Tested on ARM64, may work on other 64-bit platforms @ text @$NetBSD$ # Respect env --- Makefile.orig 2020-07-24 20:07:54.000000000 +0000 +++ Makefile @@@@ -23,9 +23,11 @@@@ INC = GCC_PREFIX = $(shell dirname `which gcc`) GCC_SUFFIX = -CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX) -CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX) -CXX = $(CPP) +CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX) +CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX) +CXX ?= $(CPP) +INSTALL ?= install + HEADERS = $(wildcard *.h) BOWTIE_MM = 1 BOWTIE_SHARED_MEM = 0 @@@@ -55,7 +57,7 @@@@ ifneq (,$(findstring Darwin,$(shell unam MACOS = 1 endif -EXTRA_FLAGS += -DPOPCNT_CAPABILITY -std=c++11 +EXTRA_FLAGS += -std=c++11 INC += -I. -I third_party MM_DEF = @@@@ -150,33 +152,11 @@@@ HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) h HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS) hisat2_repeat_main.cpp SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c) -VERSION = $(shell cat VERSION) - -# Convert BITS=?? to a -m flag -BITS=32 -ifeq (x86_64,$(shell uname -m)) -BITS=64 -endif -# msys will always be 32 bit so look at the cpu arch instead. -ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432))) - ifeq (1,$(MINGW)) - BITS=64 - endif -endif -BITS_FLAG = - -ifeq (32,$(BITS)) - BITS_FLAG = -m32 -endif - -ifeq (64,$(BITS)) - BITS_FLAG = -m64 -endif -SSE_FLAG=-msse2 +HISAT2_VERSION = $(shell cat HISAT2_VERSION) DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG) DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" -RELEASE_FLAGS = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3 +RELEASE_FLAGS = $(CXXFLAGS) RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" NOASSERT_FLAGS = -DNDEBUG FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE @@@@ -251,7 +231,7 @@@@ GENERAL_LIST = $(wildcard scripts/*.sh) MANUAL \ MANUAL.markdown \ TUTORIAL \ - VERSION + HISAT2_VERSION ifeq (1,$(WINDOWS)) HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat @@@@ -287,7 +267,7 @@@@ repeat: hisat2-repeat repeat-debug: hisat2-repeat-debug DEFS=-fno-strict-aliasing \ - -DHISAT2_VERSION="\"`cat VERSION`\"" \ + -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" \ -DBUILD_HOST="\"`hostname`\"" \ -DBUILD_TIME="\"`date`\"" \ -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \ @@@@ -517,12 +497,12 @@@@ hisat2-inspect.bat: hisat2-src: $(SRC_PKG_LIST) chmod a+x scripts/*.sh scripts/*.pl mkdir .src.tmp - mkdir .src.tmp/hisat2-$(VERSION) + mkdir .src.tmp/hisat2-$(HISAT2_VERSION) zip tmp.zip $(SRC_PKG_LIST) - mv tmp.zip .src.tmp/hisat2-$(VERSION) - cd .src.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip - cd .src.tmp ; zip -r hisat2-$(VERSION)-source.zip hisat2-$(VERSION) - cp .src.tmp/hisat2-$(VERSION)-source.zip . + mv tmp.zip .src.tmp/hisat2-$(HISAT2_VERSION) + cd .src.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip + cd .src.tmp ; zip -r hisat2-$(HISAT2_VERSION)-source.zip hisat2-$(HISAT2_VERSION) + cp .src.tmp/hisat2-$(HISAT2_VERSION)-source.zip . rm -rf .src.tmp .PHONY: hisat2-bin @@@@ -530,16 +510,16 @@@@ hisat2-bin: $(BIN_PKG_LIST) $(HISAT2_BIN chmod a+x scripts/*.sh scripts/*.pl rm -rf .bin.tmp mkdir .bin.tmp - mkdir .bin.tmp/hisat2-$(VERSION) + mkdir .bin.tmp/hisat2-$(HISAT2_VERSION) if [ -f hisat2.exe ] ; then \ zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) ; \ else \ zip tmp.zip $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) ; \ fi - mv tmp.zip .bin.tmp/hisat2-$(VERSION) - cd .bin.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip - cd .bin.tmp ; zip -r hisat2-$(VERSION)-$(BITS).zip hisat2-$(VERSION) - cp .bin.tmp/hisat2-$(VERSION)-$(BITS).zip . + mv tmp.zip .bin.tmp/hisat2-$(HISAT2_VERSION) + cd .bin.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip + cd .bin.tmp ; zip -r hisat2-$(HISAT2_VERSION)-$(BITS).zip hisat2-$(HISAT2_VERSION) + cp .bin.tmp/hisat2-$(HISAT2_VERSION)-$(BITS).zip . rm -rf .bin.tmp .PHONY: doc @@@@ -554,6 +534,20 @@@@ doc/manual.inc.html: MANUAL.markdown MANUAL: MANUAL.markdown perl doc/strip_markdown.pl < $^ > $@@ +# Install per filesystem hierarchy standard: +# https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard + +.PHONY: install +install: + mkdir -p ${DESTDIR}${PREFIX}/bin + ${INSTALL} -c -s ${HISAT2_BIN_LIST} ${DESTDIR}${PREFIX}/bin + ${INSTALL} -c hisat2 hisat2-build hisat2-inspect \ + ${DESTDIR}${PREFIX}/bin + + mkdir -p ${DESTDIR}${PREFIX}/libexec/hisat2 + ${INSTALL} -c scripts/*.sh scripts/*.pl scripts/*.py *.py \ + ${DESTDIR}${PREFIX}/libexec/hisat2 + .PHONY: clean clean: rm -f $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) \ @ 1.1 log @biology/hisat2: Update to 2.2.1 pkgsrc fix: Unbreak build on Darwin Add python3 support Several bug fixes and enhancements Changes: https://github.com/DaehwanKimLab/hisat2/tags @ text @@